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The South and SouthEast Asian freshwater fish genus Systomus (Cyprinidae) comprises 17 valid species. Six nominal species, including three endemics, have been reported from Sri Lanka, a continental island separated from India by a shallow-shelf sea. The species diversity of Systomus on the island has until now not been assessed; neither has an evaluation been made of their phylogenetic history. Here, based on an analysis of the nuclear recombination activating protein 1 (rag1), and mitochondrial cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) gene markers, and a morphological examination of 143 specimens from 49 locations in Sri Lanka, we reassess the diversity of Systomus on the island and analyse patterns of their evolution and biogeography. Divergence-time estimates, based on a substitution rate calibration, date the basal split between Systomus and its sister group, the Afrotropical small barbs, to 30.0 Ma (95% highest posterior density: 25.4-35.2 Ma). The species of Systomus belong to two distinct clades. The first includes the Sri Lankan endemics S. asoka, S. martenstyni and S. pleurotaenia, which comprise an insular diversification following the immigration of a common ancestor during the Oligocene. The second, which includes the remaining species of Indian, Sri Lankan and SouthEast Asian Systomus, has a crown age dating to the Late Miocene. Morphological and molecular species delimitation analyses failed to validate the two nominal species, S. spilurus and S. timbiri, previously reported from Sri Lanka: both are considered synonyms of S. sarana, as are the nomina S. chryseus, S. chrysopoma, S. laticeps, S. rufus, S. pinnauratus and S. subnasutus. Four genetically and geographically discrete lineages of S. sarana occur in the island, and three in India. Molecular species delimitation analysis suggests these all belong to a single species, S. sarana. The genetically distinct Sri Lankan populations of S. sarana result from Plio-Pleistocene dispersal or vicariance events between India and Sri Lanka-as a result of emergence and inundation of the now submerged isthmus connecting the two landmasses-as well as autochthonous insular diversification.

The taxonomy of the three native taxa assigned to the genus Labeo (L. dussumieri, L. fisheri and L. porcellus lankae) in Sri Lanka is reviewed. The population hitherto identified as L. dussumieri in Sri Lanka is shown to be a distinct species, here named L. heladiva. Labeo heladiva, new species, has a wide distribution in the low and mid-elevations of the island and is distinguished from its Indian congeners by the combination of having two pairs of barbels; 12–13 branched dorsal-fin rays; lateral line with 44–51 scales; ½8–½9+1+6–7 scales in transverse series; and 19–22 circumpeduncular scales. It differs from its closest relative, L. dussumieri, principally by having 44–51 vs. 50–60 lateral-line scales, 19–22 vs. 22–27 circumpeduncular scales, and by uncorrected pairwise genetic distances of 1.27–2.22% and 1.88–2.91% for the two mitochondrial genes COI and cytb, respectively. Labeo fisheri, which is endemic to the upper reaches of the Mahaweli River basin in the Knuckles mountain range and the central hills in the vicinity of Kandy, is distinguished from Indian congeners by having (in combination) only a single pair of barbels; dorsal fin with 10–12 branched rays; lateral line with 37–39 scales; 7+1+4½–6 scales in transverse series; and 17–20 circumpeduncular scales. Labeo lankae is recognized as a valid species endemic to Sri Lanka. Long suspected to have become extinct, or known only from spurious records, an extant population is reported from the northern dry zone of the island. Labeo lankae is the sister species of L. porcellus of peninsular India; it can be distinguished from its congeners by having, in combination, 10–12 branched dorsal-fin rays; 36–39 lateral-line scales; ½8+1+5–6½ scales in transverse series; and 21–24 circumpeduncular scales. It differs from L. porcellus principally by having ½8 (vs. ½6–½7) scales between the origin of the dorsal fin and the lateral line, 21–24 (vs. 20–21) circumpeduncular scales and uncorrected pairwise genetic distances of 1.27% and 1.41% for the mitochondrial genes COI and cytb, respectively. The three species of Labeo in Sri Lanka do not form a monophyletic group.

Despite exhibiting multiple morphological adaptations to living in swiftly flowing water (rheophily), Garra ceylonensis is one of the most widely distributed freshwater fish in Sri Lanka. It is thus an ideal organism to reconstruct the evolutionary history of a widespread, yet morphologically specialized, freshwater fish in a tropical-island setting. We analysed the phylogenetic and phylogeographic relationships of G. ceylonensis based on two mitochondrial and one nuclear genes. G. ceylonensis is shown to be monophyletic, with a sister-group relationship to the Indian species Garra mullya. Our results suggest a single colonization of Sri Lanka by ancestral Garra, in the late Pliocene. This suggests that the Palk Isthmus, which was exposed for most of the Pleistocene, had a hydroclimate unsuited to the dispersal of fishes such as Garra. G. ceylonensis exhibits strong phylogeographic structure: six subclades are distributed as genetically distinct populations in clusters of contiguous river basins, albeit with two exceptions. Our data reveal one or more Pleistocene extirpation events, evidently driven by aridification, with relict populations subsequently re-colonizing the island. The phylogeographic structure of G. ceylonensis suggests inter-basin dispersal largely through headwater capture, likely facilitated by free-swimming post-larvae. The Peninsular-Indian species G. mullya comprises two genetically distinct parapatric clades, which may represent distinct species.

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The taxonomic status of the large snakeheads of the Channa marulius group that occur in Sri Lanka is reviewed and clarified. Two species are recognized from the island, based on both morphological and molecular (cytochrome c oxidase subunit 1: cox1) differentiation: C. marulius Hamilton from the northern dry zone and C. ara Deraniyagala from the middle and lower regions of the Mahaweli basin. Channa ara is endemic to Sri Lanka and can be distinguished from its Marulius group congeners, C. marulius, C. aurolineata and C. auroflammea, by having fewer dorsal- and anal-fin rays, fewer lateral-line scales and fewer vertebrae; from C. marulioides by a different adult colour pattern; and from C. pseudomarulius by having more vertebrae. At the cox1 barcoding locus, Channa ara is at least 3.6% genetically different from C. marulius, and at least 8% different from the other described species in the group. Specimens collected from the southwestern wet zone in Sri Lanka are a puzzling third component of the Marulius group’s diversity, uncovered in this study, and identified here as C. cf. ara. Whilst genetically more similar to C. marulius, C. cf. ara possesses fewer dorsal- and anal-fin rays, fewer lateral-line scales and fewer vertebrae and is therefore morphologically more similar to C. ara. Channa ara can be distinguished from C. cf. ara, however, by differences in circumpeduncular scale count, adult colour pattern, and by an uncorrected pairwise genetic distance of 3.7% in cox1 sequences. A neotype is designated for Ophicephalus marulius ara Deraniyagala.

The diversity of the freshwater‐fish genus Rasbora (Cyprinidae) on Sri Lanka (five species) is high compared with the four species reported from the peninsula of India, from which the island's cyprinid fauna is derived. The paucity of characters by which species of Rasbora can be phenotypically distinguished renders field identification difficult, adversely affecting the estimation of populations and distributions, with consequences for conservation and management, increasing also the risk of taxonomic inflation. From a sampling of 90 sites across Sri Lanka and based on phylogenetic and haplotype analyses of sequences of cox1 and cytb mitochondrial, and rag1 and irbp nuclear markers, we review the species diversity and phylogeography of Rasbora on the island. Molecular analyses recover, in addition to the five species previously reported, a new (cryptic) species: Rasbora adisi sp. nov. Uncorrected pairwise cox1 genetic distances between species range from 2.0 to 12.3 percent. The Sri Lankan diversification derives from a common ancestor which arrived from India during a sea‐level low‐stand in the mid‐Miocene (15.1 Ma [95% HPD: 11.5–19.8 Ma]), when the present‐day island was subaerially connected to the Indian subcontinent by a broad isthmus. This gave rise to a clade comprising five species—R. adisi sp. nov.,Rasbora armitagei, Rasbora microcephalus, Rasbora naggsi and Rasbora wilpita—with a crown age of 9.9 Ma (95% HPD: 7.1–13.3 Ma) and to a clade comprising Indian and Sri Lankan populations of Rasbora dandia, which themselves are reciprocally monophyletic. Morphological analysis of 334 specimens discriminates between most species which, however, are most reliably diagnosed by chromatic characters. The four endemic species exhibit a pattern of inter‐basin dispersal via headwater capture, followed by vicariance, explaining the high diversity of the genus on the island.

During the past decade, the ca 120 species of small, colourful tropical Asian freshwater fishes previously referred to the cyprinid genus Puntius have been shown to consist of multiple morphologically distinct evolutionary lineages that resolve as monophyletic groups in molecular studies. Many of these clades have been allocated to new genera such as Dawkinsia, Desmopuntius, Haludaria, Oliotius, Pethia, Puntigrus, Sahyadria, Striuntius and Waikhomia. Others have been assigned to existing but previously poorly delineated genera such as Barbodes and Systomus, while some 40 species remain in Puntius. The divergent morphology of several species retained in Puntius suggests, however, that the systematics of this group requires further attention. Here, based on a phylogeny incorporating newly generated data from the mitochondrial cytochrome b (cytb), mitochondrial cytochrome c oxidase subunit 1 (cox1), nuclear recombination activating protein 1 (rag1), and interphotoreceptor retinoid‐binding protein (irbp) gene markers, we investigate the interrelationships of the species of Puntius in Sri Lanka in the wider context of their Indian and Southeast Asian congeners. We identify three well‐supported monophyletic groups that warrant recognition as new genera: Rohanella (type species Puntius titteya), Plesiopuntius (type species Gnathopogon bimaculatus) and Bhava (type species Puntius vittatus). The first of these is endemic to rainforest streams in Sri Lanka's perhumid southwestern wet zone, whereas the latter two are widely distributed in both Sri Lanka and southern India, including the Western Ghats. Our study highlights the presence of distinct evolutionary lineages among several widespread species.